tbuckley/cabot-search huggingface dataset:
Abstract 2748: Identifying therapeutic mechanism of action and new potential patient populations using PRISM
Authors: Ellen Nguyen, Shiker Nair, John Davis, Antonella Masciotti, Connor Mochi, John Finn, Cole Ponsi, Brienne Engel, Claudine Mapa, Mustafa Kocak, Melissa Ronan, Matthew G. Rees, Jennifer A. Roth
Journal: Cancer Research (2023)

Abstract Our multiplexed cell viability platform, PRISM (profiling relative inhibition simultaneously in mixtures), enables screening of potential cancer therapeutics at an unprecedented scale. We routinely assess the effects of perturbations against more than 900 cancer cell lines concurrently through the use of unique oligonucleotide barcodes stably transduced into individual cancer cell lines. Following barcode transduction, individual cell lines are pooled together in groups of 20-25 based on growth rate similarity, then thawed into 384-well assay-ready plates containing compounds of interest. After 5 days of growth, isolated mRNA is used to detect transcribed barcode abundance of each individual cancer cell line to measure relative viability. We leverage the baseline cellular features (e.g., gene expression, cell lineage, mutation, copy number, metabolomics, proteomics, genome-wide RNAi and CRISPR dependencies) of each cell line to interpret viability profiles, enabling identification of drivers of differential sensitivity and potential biomarkers of compound response. Critically, the scale and throughput of PRISM has enabled the generation of large, publicly available datasets and the rapid characterization of emerging therapeutic targets and classes (e.g., isoform-selective RAS inhibitors and degraders). Although the read-out of PRISM is relative cell line viability, the platform can be used to answer a multitude of scientific questions. For example, PRISM data can be used to identify potential patient populations who would most benefit from treatment with a specific compound, uncover unexpected off-target toxicities, and validate mechanism of action hypotheses on a more holistic scale. Ultimately, PRISM offers a large-scale and comprehensive platform for the testing and validation of anti-cancer compounds to aid in the search for new oncology therapeutics. Citation Format: Ellen Nguyen, Shiker Nair, John Davis, Antonella Masciotti, Connor Mochi, John Finn, Cole Ponsi, Brienne Engel, Claudine Mapa, Mustafa Kocak, Melissa Ronan, Matthew G. Rees, Jennifer A. Roth. Identifying therapeutic mechanism of action and new potential patient populations using PRISM [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2748.
Abstract 2963: CDX-585, a novel bispecific antibody targeting PD-1 and ILT4
Authors: Lawrence J. Thomas, Laura A. Vitale, Michael Murphy, Collin Xia, Zeyu Peng, Asma Ejas, Montu Patel, James Boyer, April R. Baronas, Thomas O'Neill, Jenifer Widger, Laura Mills-Chen, Andrea Crocker, Mark Ma, Mingjiu Chen, Hugh M. Davis, Russ A. Hammond, Cherie Taglienti, Michael Yellin, Joel Goldstein, Diego Alvarado, Henry C. Marsh, Tibor Keler
Journal: Cancer Research (2023)

Abstract Both PD-1 and ILT4 (LILRB2, CD85d) have well established immunosuppressive effects that enable tumors to evade anti-tumor immunity. Tumor expression of PD-L1 and ILT4 has been associated with poor clinical outcomes in several cancer types. Recently, ILT4 activation has been postulated as a resistance mechanism for PD-1/PD-L1 blockade prompting the investigation of dual blockade of these pathways. Siu, L.L. et al. (2022 Clin Cancer Res 28: 57-70) reported encouraging results of the initial clinical study combining the ILT4 antagonist mAb MK-4830 with pembrolizumab. The combination was generally well tolerated and led to several durable responses including in PD-1/PD-L1 refractory patients. We have combined novel PD-1 (mAb E1A9) and ILT4 (mAb 7B1) antagonist antibodies into a tetravalent IgG-scFv format bispecific antibody (bsAb, CDX-585). CDX-585 was engineered to avoid effector functionality by eliminating interaction with Fcγ receptors, and to increase its half-life by enhancing binding to FcRn. As expected, CDX-585 inhibits interaction of PD-1 and ILT4 with their ligands, results in potent inhibition of PD-1 signaling and enhances myeloid cell inflammatory responses to stimulation through toll like receptors (LPS) or CD40 (CD40 agonist mAb). In mixed lymphocyte reactions CDX-585 promoted greater T cell activation than the combination of the parental mAbs. Similarly, CDX-585 demonstrated superior anti-tumor activity over the combination of the parental mAbs in a humanized mouse model of melanoma. CDX-585 has completed GMP manufacturing and IND-enabling activities. Doses of CDX-585 up to 60 mg/kg were well tolerated in cynomolgus macaques and displayed a favorable pharmacokinetic profile. Together these data demonstrate that CDX-585 effectively combines PD-1 and ILT4 blockade into one molecule with favorable biophysical and functional characteristics supporting the initiation of a dose-escalation clinical trial in patients with advanced solid tumors. Citation Format: Lawrence J. Thomas, Laura A. Vitale, Michael Murphy, Collin Xia, Zeyu Peng, Asma Ejas, Montu Patel, James Boyer, April R. Baronas, Thomas O'Neill, Jenifer Widger, Laura Mills-Chen, Andrea Crocker, Mark Ma, Mingjiu Chen, Hugh M. Davis, Russ A. Hammond, Cherie Taglienti, Michael Yellin, Joel Goldstein, Diego Alvarado, Henry C. Marsh, Tibor Keler. CDX-585, a novel bispecific antibody targeting PD-1 and ILT4 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2963.
Abstract 2845: PpIX synthesis increases PDT resistant cells due to the modulating effect of EGCG on the heme synthesis pathway
Authors: Daniela León, Álvaro Gutiérrez, Helga Weber, Ramón Silva, María Elena Reyes, Tamara Viscarra, Kurt Buchegger, Carmen Ili, Priscilla Brebi
Journal: Cancer Research (2023)

Abstract Introduction: Photodynamic therapy (PDT) is a treatment for non melanoma skin cancer. PDT kills cells through reactive oxygen species (ROS), produced by interaction between cellular O2 and an excited photosensitizer (PS) by a specific light. One of the most used PS in dermatology is Protoporphyrin IX (PpIX) and its precursor methyl aminolevulinate (MAL). MAL enters into cells and is converted to PpIX by enzymes of the heme group synthesis pathway. The insertion of ferrous iron into PpIX forms a heme molecule, which has no PS action. A previous study shows that efficacy of PDT, in resistant cells, can be improved by addition of epigallocatechin gallate (EGCG), a green tea polyphenol. Therefore, the aim of this work is to evaluate the rol of EGCG on PPIX synthesis. Material and methods: It was used a A-431 cell line from skin squamous cell carcinoma. The EC50 of EGCG was determined by MTT assay after 24 hours. Clonogenic assay was carried out using EGCG 10, 20 and 40 μM, for 4 and 24 hours of incubation. To evaluate PpIX and ROS, A-431 cells were exposed to EGCG (10, 20, 40 μM) with or without MAL 2 mM. After 4 hours, some plates were irradiated with red light to generate ROS. PpIX and ROS were detected by flow cytometry. Gene expression of enzymes of heme synthesis was analyzed by RT-qPCR. Intracellular iron was measured using a commercial kit. ﻿ Results: EC50 determined a concentration of 50 μM of EGCG at 24 hours. EGCG concentrations from 10 μM reduced cell clonogenic capacity, even with only 4 hours of incubation. A-431 cells show PDT resistance with MAL 2 mM and a fluence of 4 J/cm2. The addition of EGCG to MAL-PDT showed a decrement of cell viability with an increase of PpIX and ROS. Besides, incubation with EGCG for 4 hours, triggered an increment of HMBS enzyme and decrease of FECH. In addition, EGCG reduced intracellular iron concentrations. Conclusion: These findings show that EGCG has a PDT enhancing effect, decreasing intracellular iron levels and modulating gene expression of heme synthesis enzymes, which are directly related with high levels of PpIX production and ROS levels, causing the death of resistant cells.Acknowledgements: Postdoctoral FONDECYT Nº 3210618, IDeA I+D FONDEF ID21I10027 Citation Format: Daniela León, Álvaro Gutiérrez, Helga Weber, Ramón Silva, María Elena Reyes, Tamara Viscarra, Kurt Buchegger, Carmen Ili, Priscilla Brebi. PpIX synthesis increases PDT resistant cells due to the modulating effect of EGCG on the heme synthesis pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2845.
Abstract 6665: A spatiotemporal cell atlas of human gastric malignancy reveals mechanisms underlying metastasis and immunotherapy response
Authors: Yikai Luo, Muxing Kang, Wei Liu, Shiping Jiao, Lie Wang, Jian Chen, Han Liang
Journal: Cancer Research (2023)

Abstract Cellular heterogeneity in the tumor immune microenvironment (TIME) of gastric cancer (GC) is progressively molded in pre- and early-malignant lesions and has a profound impact on disease progression and responses to therapeutics, in particular those based on immune checkpoint blockade (ICB). To date, no study has been conducted to characterize the single-cell kinetics of tumor-infiltrating immune populations in gastric cancer patients treated with ICB. Here, we generated for the first time single-cell RNA sequencing (scRNA-seq) and TCR sequencing (scTCR-seq) profiles of ICB-treated primary GC tumors, as well as liver and ovary metastases. When integrated with public scRNA-seq datasets, our data capture a full trajectory of GC malignancy comprising more than 300,000 cells derived from 73 samples. We further performed bulk TCR-seq, cytometry by time of flight (CyTOF), and multiplex immunofluorescence (mxIF) on independent GC samples to orthogonally validate the key observations from the scRNA-seq cohort and unbiasedly search for more in-depth and spatial-relationship-focused features of ICB-responsive immune populations. Built upon this multi-omic atlas of GC cell states, we identified remarkable transformation of the abundance and clonal dynamics of distinct immune populations and their population-specific transcriptional programs. Most importantly, we observed the rejuvenation of exhausted CD8+ T cells induced by anti-PD-1 treatment, which is associated with the enhanced immunogenicity of gastric cancer cells. In addition, we found the enrichment of NK-like terminally differentiated CD8+ T cells in metastases independent of migration destinations. Our single-cell ICB-perturbed spatiotemporal GC landscape reveals how neoadjuvant checkpoint blockade induces local and systemic tumor immunity. As a cellular and molecular reference, it also enables high-resolution interpretation of future single-cell omics data in gastric cancer that may be masked by de novo analysis. Citation Format: Yikai Luo, Muxing Kang, Wei Liu, Shiping Jiao, Lie Wang, Jian Chen, Han Liang. A spatiotemporal cell atlas of human gastric malignancy reveals mechanisms underlying metastasis and immunotherapy response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6665.
Abstract 6599: Neomer and fragmentation profiles of cell-free DNA with low-pass whole genome sequencing to predict prostate cancer biopsy outcomes
Authors: Fei Liu, Kaoqing Peng, Rui Chen, Mingzhao Li, Tao Zeng, Yan Zhao, Ming Wang, Hongxing Liu, Jianhao Wu, Min Wu, Haimeng Tang, Hua Bao, Xue Wu, Yang Shao, Di Gu, Shancheng Ren
Journal: Cancer Research (2023)

Abstract Prostate cancer is one of the most common types of cancer in men. Current prostate-specific antigen (PSA)-based diagnostic strategy for prostate cancer may frequently cause overdiagnosis. In this study, we prospectively recruited 380 individuals, including 167 with pathologically confirmed prostate cancer, 127 with negative prostate biopsy results, and 86 assessed healthy cohort with no need for biopsy. We collected a plasma sample from each participant, performed whole-genome sequencing, and profiled cell-free DNA (cfDNA) neomer and fragmentation characteristics. We then developed a machine learning model using these cfDNA profiles to predict prostate cancer biopsy outcomes. Our results showed that this assay could achieve high accuracy (Accuracy: 85.3%, AUROC: 0.919, 95% CI: 0.892 - 0.946) in repeated 5-fold cross validations. Patients with negative biopsy results had higher prediction scores than healthy individuals (P &amp;lt; 2.2X10-16), making them less distinguishable from prostate cancer patients (AUROC: 0.878, 95% CI: 0.837 - 0.918 vs. AUROC: 0.980, 95% CI: 0.963 - 0.997). We further combined this cfDNA-based assay with the PSA testing and constructed an ensemble model. The classification performance was further improved in the ensemble model, showing AUROC metrics of 0.951 (95% CI: 0.932 - 0.969) between cancer and non-cancer, 0.919 (95% CI: 0.889 - 0.949) between cancer and negative biopsy, and 0.998 (95% CI: 0.994 - 1.000) between cancer and healthy individuals. At a sensitivity of 90.4%, the ensemble assay accurately identified 85.4% of non-cancerous conditions, including 76.4% of negative biopsy patients and 98.8% of healthy individuals. We concluded that our cfDNA fragmentation and neomer-based assay could be incorporated into the PSA-based predicting system for prostate cancer to increase the accuracy and reduce the overdiagnosis. Citation Format: Fei Liu, Kaoqing Peng, Rui Chen, Mingzhao Li, Tao Zeng, Yan Zhao, Ming Wang, Hongxing Liu, Jianhao Wu, Min Wu, Haimeng Tang, Hua Bao, Xue Wu, Yang Shao, Di Gu, Shancheng Ren. Neomer and fragmentation profiles of cell-free DNA with low-pass whole genome sequencing to predict prostate cancer biopsy outcomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6599.
Abstract 4319: The need for new publication standards in cancer genomics, lessons from curating COSMIC database
Authors: Alexander Holmes, Sari A. Ward, Zbyslaw Sondka
Journal: Cancer Research (2023)

Abstract A consequence of the progress in cancer genomics is the exponential growth in data produced by research and clinical projects. Given the limited capacity within a scientific manuscript to share experimental data, various approaches have been developed: some data are simply excluded from the publication, moved to the supplementary materials, external repositories are used, and big research programmes present their integrated results on dedicated websites. This last approach has been extremely successful in generating comprehensive and unbiased datasets used by legions of scientists to discover new mechanisms driving cancer, biomarkers and drug targets. However, journal publications are still delivering more data globally, especially from rare cancers and underrepresented populations. To bring the full potential of these data and to make all this knowledge fully available, several challenges need to be addressed. COSMIC (Catalogue of Somatic Mutations in Cancer) has an in-house expert curation team that extracts information about genetic variants, their significance, patients and their response to therapy from publications and integrates it into a standardised cross-referenced database available to the scientific community. Although curators are able to extract data presented in non-standard forms (e.g. manuscript figures), interpret and translate between various data formats, they cannot extract data that are not included in the publication. Approximately one third of manuscripts that are curateable are discarded due to the absence of data generated in the research process but not included in the publication. This clearly shows an urgent need for bringing researchers, publishers, and curators together to develop new publication standards that would allow communities to fully exploit the potential of published data and make them re-usable for further discoveries. We would like to propose several suggestions to start this discussion: - Use accepted naming conventions and standards to make your data interoperable, think about your work as part of the world heritage - Include all data you generate; even if not directly relevant to the manuscript topic, they may be invaluable for somebody else’s research - Share full data and use service providers that share all the data with you - When possible, share the data per patient or sample, not per cohort - Publishing a manuscript is not an endpoint, there’s a huge potential in your data to be further utilised to fight cancer Citation Format: Alexander Holmes, Sari A. Ward, Zbyslaw Sondka. The need for new publication standards in cancer genomics, lessons from curating COSMIC database. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4319.
Abstract 177: Expansion of established patient-derived tumoroids in a novel serum-free, Wnt-free media system
Authors: Colin Paul, Brittany Balhouse, Chris Yankaskas, Shyanne Salen, Sybelle Djikeng, Pradip Shahi Thakuri, Matt Dallas, David Kuninger
Journal: Cancer Research (2023)

Abstract Tumoroid technology enables culture of patient tissue-derived cancer cells in 3D, with retention of key characteristics from the original patient tumor. However, current tumoroid culture relies on labor-intensive media formulations and culture workflows. To address these issues, we have developed the serum- and conditioned medium-free Gibco™ OncoPro™ Tumoroid Culture Medium to enable derivation and expansion of patient-derived lines from multiple cancer indications. The system has been optimized to retain key patient genotypic and phenotypic characteristics during in vitro culture in a Wnt agonist-free system that can be easily adopted and transferred between labs. To test the applicability of our system with previously established tumoroid/cancer organoid models, we procured publicly available cancer models from the National Cancer Institute Patient-Derived Models Repository (NCI PDMR). Multiple colorectal, lung, pancreas, and head and neck tumoroid models were tested, including tumoroids originally derived in conditioned medium containing Wnt-3A, R-spondin 3, and Noggin. Cells were assessed for survival, growth, and fidelity to starting material in both OncoPro Tumoroid Culture Medium and in PDMR-recommended homebrew media. Growth and morphology of tumoroid cells was monitored and was comparable between culture conditions. To test for genetic stability of cultures over time, the mutational status of organoids expanded in each condition was characterized using targeted NGS. Both SNV allelic frequency and ploidy values were conserved from initial starting material following expansion to cryopreservation-competent banks (&amp;gt;10e6 cells). Gene expression levels across over &amp;gt;20,000 human RefSeq genes were compared between culture methods and showed high (&amp;gt;0.9) correlation, and Wnt-related signaling pathways were not differentially regulated between media types. In select cases, tumoroid cells expanded in each condition were also analyzed by flow cytometry using optimized antibody panels and protocols. Total cell viability and expression of EpCAM, CD45, CD31, smooth muscle actin, vimentin, CDX2, CEACAM, and cytokeratin 7 was nearly identical across culture conditions. Taken together, our approach represents a simple and effective method to expand and maintain patient-derived human cancer organoids in vitro, with no clear adverse effects from moving to a Wnt-free system. Citation Format: Colin Paul, Brittany Balhouse, Chris Yankaskas, Shyanne Salen, Sybelle Djikeng, Pradip Shahi Thakuri, Matt Dallas, David Kuninger. Expansion of established patient-derived tumoroids in a novel serum-free, Wnt-free media system [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 177.
Abstract 4311: Using multiomics analysis to identify dysregulated transcription factors in non-small cell lung cancer (NSCLC) to drive the expression of a cancer-activated synthetic biomarker
Authors: Yue Wendy Zhang, Shireen Rudina, Dariusz Wodziak, Chloe Xia, Maggie Louie, Albert Park, David Suhy
Journal: Cancer Research (2023)

Abstract Early detection of cancer is an important driver of increased survival, quality of life and reduced healthcare costs. Earli is developing a highly sensitive, orthogonal approach that uses a genetic construct that usurps dysregulated pathways and actively forces cancer cells to drive the expression of a detectable ‘synthetic’ biomarker. Identification of abnormally elevated transcription factors (TF) in cancer is crucial when developing a cancer-activated expression platform. Evaluating TF function in a genome wide fashion is a challenge, especially since TF activity is not solely reflected by just its RNA expression or even by protein abundance, but also its post-translational modification including phosphorylation. In this study, we use the publicly available multiomics dataset from Clinical Proteomic Tumor Analysis Consortium (CPTAC) which includes RNA-seq based transcriptional profiling, MS based protein abundance and phosphorylation from 211 paired tumor and normal adjacent samples derived from NSCLC patients. Performing Multiomics Factor Analysis (MOFA) analysis, we identified a short list of 34 dysregulated TFs in NSCLC that displayed high expression levels in at least two of the three omics platforms relative to normal tissues, six of which scored highly across all three. A subset of candidate TF binding sequences were subcloned as multimers into expression constructs with a basal promoter and empirically evaluated in multiple cancer cell lines, including patient-derived xenograft (PDX) cell lines and normal cell lines.Transfection experiments demonstrated that these novel chimeric synthetic promoters could produce robust levels of expression in PDX-derived cell lines that was 10-20x higher than expression mediated by known cancer-activated promoters such as the endogenous survivin (BIRC5) promoter. Furthermore, levels achieved were only 3-4 fold lower than a control EF-1a promoter, one of the strongest promoters, typically used to drive constitutive expression in mammalian cells. Currently, a small subset of these chimeric constructs is being tested in murine tumor models and in large animal cancer models such as oncopigs. These experiments will further drive the development of this approach for use in early cancer detection. Citation Format: Yue Wendy Zhang, Shireen Rudina, Dariusz Wodziak, Chloe Xia, Maggie Louie, Albert Park, David Suhy. Using multiomics analysis to identify dysregulated transcription factors in non-small cell lung cancer (NSCLC) to drive the expression of a cancer-activated synthetic biomarker. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4311.